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Cobalt in PDB 2evo: Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide

Enzymatic activity of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide

All present enzymatic activity of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide, PDB code: 2evo was solved by W.-J.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.200, 63.400, 75.300, 90.00, 108.50, 90.00
R / Rfree (%) 21.3 / 24.1

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide (pdb code 2evo). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide, PDB code: 2evo:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in 2evo

Go back to Cobalt Binding Sites List in 2evo
Cobalt binding site 1 out of 6 in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co901

b:13.2
occ:1.00
 O A:HOH1043 2.0 12.9 1.0
OD1 A:ASP108 2.1 10.9 1.0
OE1 A:GLU235 2.1 11.5 1.0
OD1 A:ASP97 2.2 9.0 1.0
OD2 A:ASP97 2.3 12.4 1.0
O A:HOH1042 2.3 10.7 1.0
CG A:ASP97 2.5 10.1 1.0
CG A:ASP108 2.9 11.5 1.0
CD A:GLU235 3.0 11.0 1.0
OD2 A:ASP108 3.1 10.1 1.0
CO A:CO902 3.1 13.5 1.0
OE2 A:GLU235 3.2 7.5 1.0
O A:HOH915 3.7 11.7 1.0
OG1 A:THR99 4.0 9.7 1.0
O A:HOH1039 4.0 17.7 1.0
CB A:ASP97 4.0 8.0 1.0
O A:HOH1040 4.2 14.1 1.0
OE1 A:GLU204 4.2 13.0 1.0
CG A:GLU235 4.3 9.0 1.0
CB A:ASP108 4.4 9.3 1.0
O A:HOH936 4.5 17.2 1.0
OE2 A:GLU204 4.5 11.5 1.0
O A:VAL98 4.5 10.1 1.0
N A:THR109 4.5 7.5 1.0
O A:HOH930 4.6 12.5 1.0
CD A:GLU204 4.6 11.4 1.0
O A:THR109 4.7 7.5 1.0
C A:ASP108 4.7 7.8 1.0
CA A:ASP97 4.8 9.6 1.0
C A:THR109 4.8 6.6 1.0
CA A:ASP108 4.8 9.0 1.0
CB A:GLU235 4.9 7.9 1.0
N A:VAL98 4.9 8.7 1.0
CE1 A:PHE177 5.0 13.2 1.0
C A:ASP97 5.0 9.7 1.0
NE2 A:HIS171 5.0 6.5 1.0
CA A:THR109 5.0 6.8 1.0

Cobalt binding site 2 out of 6 in 2evo

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Cobalt binding site 2 out of 6 in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co902

b:13.5
occ:1.00
 O A:HOH1043 1.9 12.9 1.0
OE2 A:GLU235 2.0 7.5 1.0
NE2 A:HIS171 2.1 6.5 1.0
OE2 A:GLU204 2.1 11.5 1.0
OD2 A:ASP108 2.1 10.1 1.0
CD A:GLU235 3.0 11.0 1.0
CG A:ASP108 3.0 11.5 1.0
CD2 A:HIS171 3.0 8.6 1.0
CD A:GLU204 3.0 11.4 1.0
CE1 A:HIS171 3.1 8.8 1.0
CO A:CO901 3.1 13.2 1.0
OE1 A:GLU235 3.3 11.5 1.0
OE1 A:GLU204 3.4 13.0 1.0
OD1 A:ASP108 3.4 10.9 1.0
OG1 A:THR202 3.6 9.5 1.0
O A:HOH1031 3.9 20.1 1.0
O A:HOH1039 3.9 17.7 1.0
CG2 A:THR202 4.0 9.5 1.0
CB A:THR202 4.1 8.9 1.0
CB A:ASP108 4.1 9.3 1.0
CG A:HIS171 4.1 8.4 1.0
ND1 A:HIS171 4.1 9.0 1.0
CG A:GLU235 4.3 9.0 1.0
CG A:GLU204 4.3 10.8 1.0
O A:HOH1042 4.3 10.7 1.0
CE1 A:PHE177 4.7 13.2 1.0
NE2 A:HIS178 4.8 14.9 1.0
OD2 A:ASP97 4.9 12.4 1.0
CD2 A:HIS178 4.9 14.9 1.0
CB A:GLU204 4.9 8.3 1.0

Cobalt binding site 3 out of 6 in 2evo

Go back to Cobalt Binding Sites List in 2evo
Cobalt binding site 3 out of 6 in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co903

b:20.3
occ:1.00
 N2 A:CT0503 2.1 20.1 1.0
O A:HOH1039 2.1 17.7 1.0
NE2 A:HIS79 2.2 14.4 1.0
O A:HOH1041 2.2 12.4 1.0
O2 A:CT0503 2.2 18.8 1.0
O A:HOH1040 2.2 14.1 1.0
C1 A:CT0503 2.9 20.8 1.0
C6 A:CT0503 2.9 22.2 1.0
CD2 A:HIS79 3.1 13.0 1.0
C3 A:CT0503 3.1 19.6 1.0
CE1 A:HIS79 3.2 15.7 1.0
N A:CT0503 3.5 18.0 1.0
O A:HOH1031 3.8 20.1 1.0
O A:HOH1043 4.1 12.9 1.0
O A:CT0503 4.1 21.5 1.0
NE2 A:HIS178 4.2 14.9 1.0
CG A:HIS79 4.2 12.8 1.0
N7 A:CT0503 4.3 23.4 1.0
ND1 A:HIS79 4.3 13.2 1.0
O A:HOH930 4.3 12.5 1.0
O A:HOH1042 4.5 10.7 1.0
OD2 A:ASP97 4.6 12.4 1.0
S A:CT0503 4.7 20.7 1.0
CE1 A:HIS178 4.8 16.3 1.0
C4 A:CT0503 4.9 18.2 1.0
O A:HOH946 5.0 10.4 1.0
C8 A:CT0503 5.0 25.0 1.0

Cobalt binding site 4 out of 6 in 2evo

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Cobalt binding site 4 out of 6 in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co904

b:12.8
occ:1.00
 OD1 B:ASP108 2.1 8.8 1.0
O B:HOH1022 2.1 7.7 1.0
OD1 B:ASP97 2.1 7.2 1.0
OE1 B:GLU235 2.2 9.6 1.0
O B:HOH1023 2.3 10.8 1.0
OD2 B:ASP97 2.3 5.9 1.0
CG B:ASP97 2.5 7.1 1.0
CG B:ASP108 2.9 8.3 1.0
CD B:GLU235 3.1 8.4 1.0
OD2 B:ASP108 3.1 8.7 1.0
CO B:CO905 3.1 12.1 1.0
OE2 B:GLU235 3.2 8.4 1.0
O B:HOH916 3.7 11.4 1.0
OG1 B:THR99 3.9 8.0 1.0
CB B:ASP97 4.0 7.2 1.0
O B:HOH1021 4.1 20.6 1.0
O B:HOH1019 4.1 16.3 1.0
OE1 B:GLU204 4.2 11.4 1.0
CB B:ASP108 4.3 8.3 1.0
O B:HOH934 4.4 14.3 1.0
O B:VAL98 4.4 8.8 1.0
N B:THR109 4.5 6.3 1.0
CG B:GLU235 4.5 10.6 1.0
OE2 B:GLU204 4.5 9.6 1.0
O B:HOH920 4.5 11.7 1.0
CD B:GLU204 4.6 11.4 1.0
C B:ASP108 4.7 7.8 1.0
O B:THR109 4.8 8.1 1.0
CA B:ASP97 4.8 8.8 1.0
CA B:ASP108 4.8 9.1 1.0
C B:THR109 4.9 7.7 1.0
C B:ASP97 4.9 7.7 1.0
CB B:GLU235 5.0 8.4 1.0
N B:VAL98 5.0 7.9 1.0

Cobalt binding site 5 out of 6 in 2evo

Go back to Cobalt Binding Sites List in 2evo
Cobalt binding site 5 out of 6 in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co905

b:12.1
occ:1.00
 O B:HOH1022 2.0 7.7 1.0
OE2 B:GLU235 2.0 8.4 1.0
OD2 B:ASP108 2.1 8.7 1.0
OE2 B:GLU204 2.1 9.6 1.0
NE2 B:HIS171 2.1 6.5 1.0
CG B:ASP108 3.0 8.3 1.0
CD B:GLU235 3.0 8.4 1.0
CD B:GLU204 3.0 11.4 1.0
CE1 B:HIS171 3.1 8.4 1.0
CD2 B:HIS171 3.1 8.2 1.0
CO B:CO904 3.1 12.8 1.0
OE1 B:GLU204 3.3 11.4 1.0
OE1 B:GLU235 3.3 9.6 1.0
OD1 B:ASP108 3.4 8.8 1.0
OG1 B:THR202 3.5 6.5 1.0
O B:HOH1021 3.8 20.6 1.0
CG2 B:THR202 3.9 8.0 1.0
CB B:THR202 4.0 6.8 1.0
CB B:ASP108 4.1 8.3 1.0
ND1 B:HIS171 4.2 7.7 1.0
CG B:HIS171 4.2 7.6 1.0
O B:HOH1023 4.3 10.8 1.0
CG B:GLU235 4.3 10.6 1.0
CG B:GLU204 4.3 9.7 1.0
CE1 B:PHE177 4.7 7.6 1.0
OD2 B:ASP97 4.9 5.9 1.0
NE2 B:HIS178 4.9 11.7 1.0
CB B:GLU204 4.9 7.7 1.0
CD2 B:HIS178 4.9 13.2 1.0

Cobalt binding site 6 out of 6 in 2evo

Go back to Cobalt Binding Sites List in 2evo
Cobalt binding site 6 out of 6 in the Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Methionine Amino Peptidase in Complex with N-Cyclopentyl-N-(Thiazol-2-Yl)Oxalamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co906

b:17.9
occ:1.00
 N2 B:CT0502 2.1 16.8 1.0
O2 B:CT0502 2.1 17.5 1.0
O B:HOH1019 2.2 16.3 1.0
NE2 B:HIS79 2.2 18.4 1.0
O B:HOH1021 2.2 20.6 1.0
O B:HOH1020 2.3 18.3 1.0
C1 B:CT0502 2.8 18.2 1.0
C6 B:CT0502 2.8 18.1 1.0
CD2 B:HIS79 3.0 18.3 1.0
C3 B:CT0502 3.1 16.6 1.0
CE1 B:HIS79 3.3 19.0 1.0
N B:CT0502 3.5 14.9 1.0
O B:HOH1022 4.0 7.7 1.0
O B:CT0502 4.1 18.0 1.0
NE2 B:HIS178 4.1 11.7 1.0
N7 B:CT0502 4.2 21.6 1.0
CG B:HIS79 4.2 15.6 1.0
O B:HOH920 4.3 11.7 1.0
ND1 B:HIS79 4.3 17.5 1.0
O B:HOH1023 4.5 10.8 1.0
OD2 B:ASP97 4.6 5.9 1.0
S B:CT0502 4.7 17.0 1.0
CE1 B:HIS178 4.8 13.3 1.0
C4 B:CT0502 4.9 14.2 1.0
C8 B:CT0502 4.9 24.1 1.0
O B:HOH938 5.0 12.7 1.0

Reference:

S.X.Xie, W.J.Huang, Z.Q.Ma, M.Huang, R.P.Hanzlik, Q.Z.Ye. Structural Analysis of Metalloform-Selective Inhibition of Methionine Aminopeptidase. Acta Crystallogr.,Sect.D V. 62 425 2006.
ISSN: ISSN 0907-4449
PubMed: 16552144
DOI: 10.1107/S0907444906003878
Page generated: Tue Jul 30 15:07:16 2024

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